7-deaza-8-aza-deoxyguanosine (deaza G (PPG)) is a deoxyribonucleoside in which the 7-nitrogen and 8-carbon are flipped. The resulting modified dG is unable to form a hydrogen bond at position 7, but can at position 8. The result is that the 7-deaza-8-aza-G : C base pair increases the stability of the duplex by about 1 degC in Tm compared with the unmodified G : C base pair (1, 2). Similar to 7-deaza-dG, 7-deaza-8-aza-dG can be used to reduce structural problems posed by G-rich and GC-rich regions. Because such regions can form non-Watson-Crick hydrogen bonds, they can form highly stable secondary structures (such as G-qudraplex) that effectively prevent generation of PCR products (or even readable DNA sequence) from them (3). Because it cannot form hydrogen bonds at position 7, substitution of 7-deaza-8-aza-dG at certain dG positions in G- or GC-rich oligos slated for use in PCR as either PCR primers or templates can reduce these secondary structures and thus improve PCR product generation (4). In addition, because the higher thermodynamic stability improves discrimination of G:A, G:G; and G:T mismatches in DNA duplexes, the 7-deaza-8-aza-dG modification makes the use of G-rich DNA probes a viable option for diagnostic assays (4).
References
1. Seela, F.; Driller, H. 8-Aza-7-deaza-2’-deoxyguanosine: Phosphoramidite synthesis and properties of octanucleotides. Helv. Chim. Acta. (1988), 71: 1191-1198.
2. Seela, F.; Driller, H. Alternating d(G-C)3 and d(C-G)3 hexanucleotides containing 7-deaza-2’-deoxyguanosine or 8-aza-7-deaza-2’-deoxyguanosine in place of dG. Nucleic Acids Res. (1989), 17: 901-910.
3. Fernandez-Rachubinski, F.; Murray, W.W.; Blajchman, M.A.; Rachubinski, R.A. Incorporation of 7-deaza dGTP during the amplification step in the polymerase chain reaction procedure improves subsequent DNA sequencing.DNA Seq. (1990), 1: 137-140.
4. Kutyavin, I.V.; Lokhov, S.G.; Afonina, I.A.; Dempcy, R., et al. Reduced aggregation and improved specificity of G-rich oligodeoxyribonucleotides containing pyrazolo[3,4-d]pyrimidine guanine bases.Nucleic Acids Res. (2002), 30: 4952-4959.
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